Showing : glm • reset
2
votes
3
replies
101
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 1 day ago by 50k • written 1 day ago by • 0
1
vote
1
reply
790
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 23 months ago by 42k • written 23 months ago by • 0
3
votes
6
replies
1.0k
views
EdgeR design matrix with 3 factors
edgeR glm RNAseq
updated 3.7 years ago by 65k • written 3.7 years ago by • 0
1
vote
6
replies
888
views
Rescaling predictors in DESeq changes outcomes?
deseq2 glm rescale
updated 4.0 years ago by 42k • written 4.0 years ago by ▴ 10
6
votes
6
replies
1.2k
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 4.3 years ago by ★ 13k • written 4.3 years ago by • 0
0
votes
1
reply
902
views
Assessing the influence of covariates on RNA-seq in DESeq2
deseq2 rna-sequencing covariates glm
updated 4.4 years ago by 42k • written 4.4 years ago by ▴ 20
0
votes
1
reply
1.1k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 4.5 years ago by 42k • written 4.5 years ago by • 0
7
votes
5
replies
1.7k
views
EdgeR - Complex design - contrasts/coefficients
edger GLM
updated 4.7 years ago by ▴ 840 • written 4.7 years ago by ▴ 10
1
vote
6
replies
1.7k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
4.7 years ago sabrina.mcnew • 0
0
votes
2
replies
881
views
NanoStringDiff correction for variation between patient
NanoStringDiff GLM Gene expression
updated 4.7 years ago by 65k • written 4.7 years ago by • 0
0
votes
3
replies
1.2k
views
ROC curves using normalized sequencing data from 2 experiments
deseq2 pROC ROCR glm
4.9 years ago sebastian.lobentanzer ▴ 50
0
votes
0
replies
850
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
4.9 years ago garbuzov • 0
2
votes
8
replies
1.6k
views
Differential gene expression using edgeR and using a generalised linear model (GLM)
edger GLM
updated 5.0 years ago by ★ 28k • written 5.0 years ago by • 0
4
votes
7
replies
1.2k
views
EdgeR between/within comparisons (3.5) with nested non-balanced data set
edgeR nested glm glmQLFit
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 10
2
votes
2
replies
887
views
edgeR DEG how many treatments should be fitted to GLM
edgeR GLM
updated 5.3 years ago by 50k • written 5.3 years ago by ▴ 10
0
votes
1
reply
1.1k
views
merging RUV-corrected datasets in DESEq
deseq2 glm zinbwave ruvseq
updated 5.4 years ago by 42k • written 5.4 years ago by ▴ 50
2
votes
2
replies
1.0k
views
edgeR DE analysis: single group combined factors or GLM with interaction term
edger glm
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 10
1
vote
3
replies
1.3k
views
Help interpreting DESeq2 method for gene-wide dispersion estimates
deseq2 negative binomial model glm
updated 5.8 years ago by 42k • written 5.8 years ago by • 0
9
votes
1
reply
4.4k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2 model.matrix GLM contrast
updated 6.3 years ago by 42k • written 6.3 years ago by ▴ 60
6
votes
6
replies
8.1k
views
EdgeR design matrix with 3 factors
edger glm rnaseq
6.4 years ago Denniswu ▴ 20
4
votes
7
replies
2.7k
views
GLM model on time course analysis and removing the outliers in Deseq2
deseq2 GLM timecourse
updated 6.5 years ago by 42k • written 7.4 years ago by ▴ 10
5
votes
4
replies
1.4k
views
interpretation of edgeR multi factor conditions in GLM
edger multivariate multiple factor design glm
updated 7.0 years ago by ★ 7.9k • written 7.0 years ago by • 0
2
votes
1
reply
1.2k
views
diffHiC with no biological replicates?
diffhic estimate dispersion value glm no replicates deseq
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 20
1
vote
2
replies
1.5k
views
Trying to design a model(s) for a two factor RNA-seq experimental analysis in EdgeR with interaction
EdgeR RNAseq experimental design glm
updated 7.2 years ago by ★ 28k • written 7.2 years ago by • 0
1
vote
2
replies
1.0k
views
Treating 2 coefficients as the same group in Limma
limma glm
updated 7.6 years ago by 65k • written 7.6 years ago by ▴ 50
3
votes
2
replies
5.9k
views
QLF or LRT in edgeR for paired sample designs?
edger paired samples glm QL F-test LR-test
updated 7.7 years ago by ★ 28k • written 7.7 years ago by • 0
11
votes
3
replies
1.8k
views
Fit a multinomial to RNA-seq count data
voom limma glm multinomial regression
updated 7.8 years ago by ★ 3.3k • written 7.8 years ago by ▴ 110
3
votes
1
reply
5.3k
views
edgeR: exactTest, glmFIt or glmQLFit approach?
edger rnaseq glm glmfit
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
9
votes
7
replies
1.7k
views
EdgeR returns small logFC values when using GLM approach
edger glm logfc
8.1 years ago gergely.zsuzsa.n • 0
1
vote
1
reply
1.5k
views
edgeR, DE between 4 different samples
edger differential gene expression GLM Tutorial
updated 8.1 years ago by 65k • written 8.1 years ago by • 0
18
votes
10
replies
7.1k
views
Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
edger estimatedispersions glm
updated 8.2 years ago by 50k • written 8.2 years ago by ▴ 180
1
vote
1
reply
2.3k
views
edgeR GLM fitted values
edgeR GLM classification rnaseq
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 10
0
votes
4
replies
1.2k
views
edgeR GLM design question: contrasts
edger GLM
8.3 years ago jwi • 0
2
votes
2
replies
2.5k
views
order of covariates for GLM with edgeR
edger differential expression covariate batch effect glm
updated 8.4 years ago by 50k • written 8.4 years ago by ▴ 90
11
votes
11
replies
3.3k
views
Different results in edgeR using simple vs GLM
edger glm rnaseq
8.6 years ago dietahanson ▴ 30
2
votes
12
replies
2.5k
views
LAPACK/BLAS error with edgeR GLM
glm edger lapack segfault ruvseq
8.8 years ago Mark.Rogers • 0
6
votes
8
replies
2.8k
views
edgeR vs glm.nb
edgeR glm
8.8 years ago dongamit123 ▴ 20
8
votes
4
replies
5.8k
views
Multiple Comparisons EdgeR
edger multiple comparisons anova glm
updated 8.9 years ago by ★ 7.9k • written 8.9 years ago by ▴ 20
10
votes
10
replies
7.0k
views
GLM Likelihood ratio test
rnaseq edgeR GLM
updated 9.2 years ago by 50k • written 9.2 years ago by • 0
6
votes
2
replies
1.3k
views
help for designing a multifactorial GLM framework edgeR
edgeR GLM
updated 9.5 years ago by ★ 28k • written 9.5 years ago by • 0
40 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
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Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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